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Aliases for PSD4 Gene

Aliases for PSD4 Gene

  • Pleckstrin And Sec7 Domain Containing 4 2 3 5
  • Exchange Factor For ADP-Ribosylation Factor Guanine Nucleotide Factor 6 B 3 4
  • Pleckstrin Homology And SEC7 Domain-Containing Protein 4 3 4
  • Telomeric Of Interleukin-1 Cluster Protein 3 4
  • Exchange Factor For ARF6 B 3 4
  • EFA6B 3 4
  • TIC 3 4
  • Exchange Factor For ADP-Ribosylation Factor Guanine Nucleotide Factor 6B 3
  • ADP-Ribosylation Factor Guanine Nucleotide-Exchange Factor 6 3
  • PH And SEC7 Domain-Containing Protein 4 3
  • SEC7 Homolog 3

External Ids for PSD4 Gene

Previous GeneCards Identifiers for PSD4 Gene

  • GC00U916999
  • GC02P113647
  • GC02P113914
  • GC02P106385

Summaries for PSD4 Gene

GeneCards Summary for PSD4 Gene

PSD4 (Pleckstrin And Sec7 Domain Containing 4) is a Protein Coding gene. Among its related pathways are Endocytosis. Gene Ontology (GO) annotations related to this gene include phospholipid binding and ARF guanyl-nucleotide exchange factor activity. An important paralog of this gene is PSD.

UniProtKB/Swiss-Prot for PSD4 Gene

  • Guanine nucleotide exchange factor for ARF6 and ARL14/ARF7. Through ARL14 activation, controls the movement of MHC class II-containing vesicles along the actin cytoskeleton in dendritic cells. Involved in membrane recycling. Interacts with several phosphatidylinositol phosphate species, including phosphatidylinositol 3,4-bisphosphate, phosphatidylinositol 3,5-bisphosphate and phosphatidylinositol 4,5-bisphosphate.

Additional gene information for PSD4 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PSD4 Gene

Genomics for PSD4 Gene

GeneHancer (GH) Regulatory Elements for PSD4 Gene

Promoters and enhancers for PSD4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I113172 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 589.6 +17.6 17613 4.9 HDGF PKNOX1 ATF1 SMAD1 IRF4 POLR2B CBX5 E2F8 ZNF143 ATF7 PSD4 ENSG00000234174 PAX8
GH02I113155 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 550.8 +0.5 455 3.7 FOXA2 MLX ARID4B ZNF48 YY1 GLIS2 RXRA NFYC REST ZNF623 PSD4 IL1RN PAX8-AS1 RNU6-1180P IL36RN IL36B IL1B IL36G ENSG00000234174
GH02I113178 Enhancer 1.3 Ensembl ENCODE dbSUPER 46.6 +23.1 23085 4.4 FOXA2 MLX ARID4B ZNF48 YY1 SLC30A9 RXRA NFYC ZHX2 MXD4 PSD4 PAX8-AS1 ENSG00000234174 GC02P113496 GC02P113390
GH02I113126 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 22.5 -28.1 -28072 5.1 FOXA2 MLX ARID4B DMAP1 ZNF48 ETS1 YY1 SLC30A9 PAF1 RXRA IL1RN PSD4 PAX8-AS1 RNU6-1180P PAX8 IL1F10 IL36RN LINC01191 GC02P113568 GC02P113379
GH02I113123 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19 -32.3 -32341 3.2 HDAC1 ELF3 PKNOX1 MLX BATF DNMT3B RARA RFX5 ETV6 FOS IL1RN IL36B PSD4 IL1B RNU6-1180P PAX8-AS1 PAX8 IL1F10 IL36G IL1A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PSD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PSD4 gene promoter:

Genomic Locations for PSD4 Gene

Genomic Locations for PSD4 Gene
chr2:113,157,325-113,209,396
(GRCh38/hg38)
Size:
52,072 bases
Orientation:
Plus strand
chr2:113,914,902-113,966,973
(GRCh37/hg19)

Genomic View for PSD4 Gene

Genes around PSD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PSD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PSD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PSD4 Gene

Proteins for PSD4 Gene

  • Protein details for PSD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NDX1-PSD4_HUMAN
    Recommended name:
    PH and SEC7 domain-containing protein 4
    Protein Accession:
    Q8NDX1
    Secondary Accessions:
    • A6NEG7
    • A8K1Y0
    • O95621
    • Q4ZG34
    • Q6GPH8
    • Q8IYP4

    Protein attributes for PSD4 Gene

    Size:
    1056 amino acids
    Molecular mass:
    116249 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PSD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PSD4 Gene

Post-translational modifications for PSD4 Gene

No Post-translational modifications

No data available for DME Specific Peptides for PSD4 Gene

Domains & Families for PSD4 Gene

Gene Families for PSD4 Gene

Suggested Antigen Peptide Sequences for PSD4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PSD4: view

No data available for UniProtKB/Swiss-Prot for PSD4 Gene

Function for PSD4 Gene

Molecular function for PSD4 Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor for ARF6 and ARL14/ARF7. Through ARL14 activation, controls the movement of MHC class II-containing vesicles along the actin cytoskeleton in dendritic cells. Involved in membrane recycling. Interacts with several phosphatidylinositol phosphate species, including phosphatidylinositol 3,4-bisphosphate, phosphatidylinositol 3,5-bisphosphate and phosphatidylinositol 4,5-bisphosphate.

Phenotypes From GWAS Catalog for PSD4 Gene

Gene Ontology (GO) - Molecular Function for PSD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005086 ARF guanyl-nucleotide exchange factor activity IEA --
GO:0005543 phospholipid binding IEA --
GO:0008289 lipid binding IEA --
genes like me logo Genes that share ontologies with PSD4: view
genes like me logo Genes that share phenotypes with PSD4: view

Animal Model Products

CRISPR Products

miRNA for PSD4 Gene

miRTarBase miRNAs that target PSD4

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PSD4 Gene

Localization for PSD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PSD4 Gene

Cell membrane. Cell projection, ruffle membrane. Note=In interphase associated with the plasma membrane, in particular with membrane ruffling regions (PubMed:23603394). Accumulates in dynamic actin-rich membrane ruffles and microvilli-like structures (PubMed:12082148). Recruited to membranes via phosphatidylinositol phosphate-binding (Probable). {ECO:0000269 PubMed:12082148, ECO:0000269 PubMed:23603394, ECO:0000305 PubMed:12082148}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PSD4 gene
Compartment Confidence
plasma membrane 5
cytosol 3
nucleus 2

Gene Ontology (GO) - Cellular Components for PSD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane HDA,IEA 19946888
GO:0032154 NOT cleavage furrow IDA 23603394
GO:0032587 ruffle membrane IDA,IEA 23603394
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with PSD4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PSD4 Gene

Pathways & Interactions for PSD4 Gene

SuperPathway Contained pathways
1 Endocytosis
genes like me logo Genes that share pathways with PSD4: view

Pathways by source for PSD4 Gene

1 KEGG pathway for PSD4 Gene

Gene Ontology (GO) - Biological Process for PSD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032012 regulation of ARF protein signal transduction IEA --
GO:0065009 regulation of molecular function IEA --
genes like me logo Genes that share ontologies with PSD4: view

No data available for SIGNOR curated interactions for PSD4 Gene

Drugs & Compounds for PSD4 Gene

(3) Drugs for PSD4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with PSD4: view

Transcripts for PSD4 Gene

Unigene Clusters for PSD4 Gene

Pleckstrin and Sec7 domain containing 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PSD4 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c · 13d ^ 14a · 14b ^ 15a · 15b ^ 16a ·
SP1: - - - - - - - -
SP2: - - - - - - -
SP3: - - - - - -
SP4: - - - - - -
SP5: - - - - -
SP6: - - -
SP7: -
SP8: - -
SP9: -
SP10: - - -
SP11: - -
SP12:
SP13:

ExUns: 16b ^ 17a · 17b ^ 18a · 18b · 18c · 18d · 18e
SP1: -
SP2: -
SP3: -
SP4: -
SP5: - -
SP6:
SP7: -
SP8: - -
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for PSD4 Gene

GeneLoc Exon Structure for
PSD4
ECgene alternative splicing isoforms for
PSD4

Expression for PSD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PSD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PSD4 Gene

This gene is overexpressed in Whole Blood (x11.8).

Protein differential expression in normal tissues from HIPED for PSD4 Gene

This gene is overexpressed in Plasma (28.7), Pancreas (11.7), Peripheral blood mononuclear cells (8.6), and CD8 Tcells (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PSD4 Gene



Protein tissue co-expression partners for PSD4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PSD4 Gene:

PSD4

SOURCE GeneReport for Unigene cluster for PSD4 Gene:

Hs.516306

mRNA Expression by UniProt/SwissProt for PSD4 Gene:

Q8NDX1-PSD4_HUMAN
Tissue specificity: Widely expressed. Highest levels of expression are found in placenta, pancreas, spleen, thymus and peripheral blood.

Evidence on tissue expression from TISSUES for PSD4 Gene

  • Blood(4.3)
  • Liver(4.3)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with PSD4: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PSD4 Gene

Orthologs for PSD4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PSD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PSD4 33 34
  • 92.57 (n)
dog
(Canis familiaris)
Mammalia PSD4 33 34
  • 82.09 (n)
cow
(Bos Taurus)
Mammalia PSD4 33 34
  • 81.94 (n)
rat
(Rattus norvegicus)
Mammalia Psd4 33
  • 77.19 (n)
mouse
(Mus musculus)
Mammalia Psd4 33 16 34
  • 77.08 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PSD4 34
  • 58 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PSD4 34
  • 54 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Efa6 34
  • 20 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea efa-6 34
  • 25 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEA1 34
  • 8 (a)
ManyToMany
GEA2 34
  • 8 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 22 (a)
OneToMany
Species where no ortholog for PSD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for PSD4 Gene

ENSEMBL:
Gene Tree for PSD4 (if available)
TreeFam:
Gene Tree for PSD4 (if available)

Paralogs for PSD4 Gene

(2) SIMAP similar genes for PSD4 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PSD4: view

Variants for PSD4 Gene

Sequence variations from dbSNP and Humsavar for PSD4 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000054533 -- 113,156,538(+) T/C upstream_transcript_variant
rs1000074046 -- 113,156,250(+) G/C upstream_transcript_variant
rs1000103257 -- 113,190,689(+) A/G intron_variant
rs1000153480 -- 113,161,391(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000187401 -- 113,197,454(+) G/A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PSD4 Gene

Variant ID Type Subtype PubMed ID
nsv582711 CNV loss 21841781
nsv582712 CNV loss 21841781
nsv961871 CNV duplication 23825009

Variation tolerance for PSD4 Gene

Residual Variation Intolerance Score: 61.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.98; 60.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PSD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PSD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PSD4 Gene

Disorders for PSD4 Gene

Additional Disease Information for PSD4

No disorders were found for PSD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PSD4 Gene

Publications for PSD4 Gene

  1. A conserved C-terminal domain of EFA6-family ARF6-guanine nucleotide exchange factors induces lengthening of microvilli-like membrane protrusions. (PMID: 12082148) Derrien V … Chavrier P (Journal of cell science 2002) 2 3 4 58
  2. EFA6 activates Arf6 and participates in its targeting to the Flemming body during cytokinesis. (PMID: 23603394) Ueda T … Nakayama K (FEBS letters 2013) 3 4 58
  3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for PSD4 Gene

Sources for PSD4 Gene

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